[chimerax-users] No cc when using fitmap
Tom Goddard
goddard at sonic.net
Mon Jan 10 16:44:29 PST 2022
Hi Yumeng,
I added the measure correlation command to ChimeraX to measure the correlation between two maps. For example,
open 30831 from emdb
open 30832 from emdb
measure correlation #1 inMap #2 envelope true
> Correlation of emdb 30831 #1 above level 0.2638 in emdb 30832 #2
> correlation = 0.5287, correlation about mean = 0.0983
To measure the correlation between an atomic model and a map you would first have to use the "molmap" command to compute a map from the atomic model, for example,
open 7dsd
molmap #1 2.9
open 30831 from emdb
measure corr #2 in #3
> Correlation of 7dsd map 2.9 #2 above level 0.1137 in emdb 30831 #3
> correlation = 0.7731, correlation about mean = 0.3795
Tom
> On Jan 10, 2022, at 3:38 PM, Tom Goddard via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>
> Hi Yumeng,
>
> I would not expect any difference in the correlation coefficient between Windows and Linux or with a large map versus a small map.
>
> First the command you listed does not do any fitting since you use "shift false rotate false" which does not allow the model to move.
>
> fitmap #2 inMap #1 resolution 4.0 metric correlation shift false rotate false
>
> So I assume you are doing this just to measure the correlation coefficient. And your output says the correlation coefficient is 0. That most likely means the atomic model is not located in the map. Why don't you just do the same steps in gui mode and see what happens -- it should produce exactly the same result as nogui mode. Also note that the displayed surface level matters because by default fitmap only uses data above the contour level of the displayed surface of the map you are fitting into. That actually may explain why your large map case did not work, because if you open a large map ChimeraX may initially just show a single plane in gray scale instead of a surface, and with no surface it won't have a surface level. So to get a predictable result you should use the volume command to show a surface of the full map and set the threshold level you want to use, for example,
>
> volume #1 style surface region all level 0.2
>
> I see that ChimeraX does not have the "measure correlation" command that is in the older Chimera program. I will try to add that.
>
> Tom
>
>
>
>
>> On Jan 10, 2022, at 2:14 PM, Yumeng Yan via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>>
>> Hi,
>>
>> When I tried to use fitmap function ChimeraX in Linux with --nogui option, I got no CC output when the Cryo-EM map is large(1.6GB) and I think in this situation, the local fit did not work. When the map was cut of a half size, it works. But it works well on Windows. Could you help me?
>>
>> Here are the commands:
>> open ../Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc fit_11.pdb
>> fitmap #2 inMap #1 resolution 4.0 metric correlation shift false rotate false
>>
>> Here is the log information:
>> INFO:
>> UCSF ChimeraX version: 1.4.dev202201082018 (2022-01-08)
>> INFO:
>> © 2016-2021 Regents of the University of California. All rights reserved.
>> INFO:
>> Executing: open .33092SymAndFit.cxc
>> INFO:
>> Executing: open ../Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc fit_11.pdb
>> STATUS:
>> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 0%
>> STATUS:
>> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 8%
>> STATUS:
>> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 16%
>> STATUS:
>> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 24%
>> STATUS:
>> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 32%
>> STATUS:
>> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 40%
>> STATUS:
>> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 48%
>> STATUS:
>> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 56%
>> STATUS:
>> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 64%
>> STATUS:
>> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 72%
>> STATUS:
>> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 80%
>> STATUS:
>> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 87%
>> STATUS:
>> Done reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc
>> STATUS:
>> Computing histogram for Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc
>> STATUS:
>> Computing Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc surface, level 0.292
>> STATUS:
>> Calculated Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc surface, level 0.292, with 10911480 triangles
>> INFO:
>> Opened Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc as #1, grid size 750,750,750, pixel 1.1, shown at level 0.292, step 1, values float32
>> INFO:
>> Chain information for fit_11.pdb #2
>> ---
>> Chain | Description
>> [F](cxcmd:select /F:2-219 "Select chain") | [No description
>> available](cxcmd:sequence chain #2/F "Show sequence")
>>
>>
>> INFO:
>> Executing: fitmap #2 inMap #1 resolution 8.0 metric correlation shift false rotate false
>> INFO:
>> Opened fit_11.pdb map 8 as #3, grid size 40,42,43, pixel 2.67, shown at level 0.0533, step 1, values float32
>> INFO:
>> Fit map fit_11.pdb map 8 in map Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc using 2211 points
>> correlation = 0, correlation about mean = 0, overlap = 0
>> steps = 24, shift = 0, angle = 0 degrees
>>
>> INFO:
>> Position of fit_11.pdb map 8 (#3) relative to Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc (#1) coordinates:
>> Matrix rotation and translation
>> 1.00000000 0.00000000 0.00000000 0.00000000
>> 0.00000000 1.00000000 0.00000000 0.00000000
>> 0.00000000 0.00000000 1.00000000 0.00000000
>> Axis 0.00000000 0.00000000 1.00000000
>> Axis point 0.00000000 0.00000000 0.00000000
>> Rotation angle (degrees) 0.00000000
>> Shift along axis 0.00000000
>>
>> STATUS:
>> 24 steps, shift 0, rotation 0 degrees, correlation 0.0000
>>
>>
>> Best wishes,
>> Yumeng
>>
>> Yumeng Yan
>> Postdoctoral Fellow
>>
>> Taylor and Rasmussen Group
>> University of Copenhagen
>> Faculty of Health and Medical Sciences
>> Novo Nordisk Foundation Center for Protein Research
>>
>> Blegdamsvej 3B, building 6
>> 2200 Copenhagen N
>> DENMARK
>>
>> yumeng.yan at cpr.ku.dk <mailto:yumeng.yan at cpr.ku.dk>
>>
>> <OutlookEmoji-1638361915486c0a23484-e68c-4b46-9d5a-75949bd8128d.png>
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